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- PDB-2hvz: Solution structure of the RRM domain of SR rich factor 9G8 -

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Basic information

Entry
Database: PDB / ID: 2hvz
TitleSolution structure of the RRM domain of SR rich factor 9G8
ComponentsSplicing factor, arginine/serine-rich 7
KeywordsRNA BINDING PROTEIN / RRM
Function / homology
Function and homology information


mRNA 3'-end processing / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / RNA Polymerase II Transcription Termination / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Minor Pathway / negative regulation of mRNA splicing, via spliceosome / mRNA export from nucleus ...mRNA 3'-end processing / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA export from nucleus / RNA Polymerase II Transcription Termination / regulation of alternative mRNA splicing, via spliceosome / mRNA Splicing - Minor Pathway / negative regulation of mRNA splicing, via spliceosome / mRNA export from nucleus / mRNA Splicing - Major Pathway / RNA splicing / cellular response to leukemia inhibitory factor / mRNA splicing, via spliceosome / mRNA processing / nuclear speck / protein domain specific binding / RNA binding / zinc ion binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SRSF7, RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. ...SRSF7, RNA recognition motif / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Serine/arginine-rich splicing factor 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsTintaru, A.M. / Hautbergue, G.M. / Golovanov, A.P. / Lian, L.Y. / Wilson, S.A.
CitationJournal: Embo J. / Year: 2006
Title: Molecular basis of RNA recognition and TAP binding by the SR proteins SRp20 and 9G8.
Authors: Hargous, Y. / Hautbergue, G.M. / Tintaru, A.M. / Skrisovska, L. / Golovanov, A.P. / Stevenin, J. / Lian, L.Y. / Wilson, S.A. / Allain, F.H.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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MolmilJmol/JSmol

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Assembly

Deposited unit
A: Splicing factor, arginine/serine-rich 7


Theoretical massNumber of molelcules
Total (without water)11,3391
Polymers11,3391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Splicing factor, arginine/serine-rich 7 / Splicing factor 9G8


Mass: 11338.986 Da / Num. of mol.: 1 / Fragment: RRM (amino acids K12-R98)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFRS7 / Plasmid: pET24b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21/RP / References: UniProt: Q16629

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1312D TOCSY
NMR detailsText: The 9G8 sequence starts at K2 and finishes at R88, corresponding to K12 and R98, respectively. All the other amino-acids are part of the T7 and histidine tags.

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Sample preparation

DetailsContents: NMR sample: 13C, 15N-9G8 RRM at 0.6 mM Buffer conditions: 20mM CH3COONa (pH=5.5), 25mM L-ARG, 50mM L-Glu, 5mM EDTA, 10mM DTT; 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 293 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5collection
NMRPipe1F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
NMRView5.01B.A.Johnson and R.A.Blevinsdata analysis
CYANA2.1P.Guntert, C.Mumenthaler and K. Wuthrich,structure solution
Amber7Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJrefinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1138 restraints, 951 are NOE-derived distance constraints, 119 dihedral angle restraints and 68 distance restraints from hydrogen bonds
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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